Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,127,431 |
C→T |
pseudogene (747/1425 nt) |
tssA → |
type VI secretion system protein TssA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,127,431 | 0 | C | T | 100.0%
| 31.9
/ NA
| 19 | pseudogene (747/1425 nt) | tssA | type VI secretion system protein TssA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (3/16); total (3/16) |
CAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCAT > NC_017635/3127408‑3127473
|
cAGGCCGACCTGATGTTCAGCTCTGGCGTCAGCCATTTCTGGCTGGAc < 1:877298/48‑1 (MQ=11)
cAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGAc < 2:2447520/48‑1 (MQ=255)
aGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACa < 2:220635/48‑1 (MQ=255)
cGACCTGATGTTCAGCACTGGCGTCAGCCAATTCTGGCTGGACATTCa < 2:1988982/48‑1 (MQ=11)
gATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa > 2:1223024/1‑48 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt < 1:1071073/46‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt < 2:409153/46‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:510618/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:2548815/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 2:1950593/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:399710/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:320729/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa < 1:1360315/47‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt < 1:2133545/48‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt < 2:60274/48‑1 (MQ=11)
gTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCt > 2:1307723/1‑48 (MQ=11)
cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc < 2:701923/47‑1 (MQ=11)
cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc < 1:1308586/47‑1 (MQ=11)
cACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCAt > 2:2552346/1‑46 (MQ=11)
|
CAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCAT > NC_017635/3127408‑3127473
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGCAGAACTGGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGC > NC_017635/3127381‑3127480
|
CAGCAGAACTGGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACT < M01420:84:000000000‑ABVEH:1:2113:16094:8160/51‑1 (MQ=0)
AGCAGAACTGGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACTG > M01420:84:000000000‑ABVEH:1:1113:23556:17927/1‑51 (MQ=0)
AGCAGAACTGGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACCG < M01420:84:000000000‑ABVEH:1:1106:14123:9643/51‑1 (MQ=0)
GGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCC > M01420:84:000000000‑ABVEH:1:2107:17113:5190/1‑51 (MQ=0)
ACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCAT < M01420:84:000000000‑ABVEH:1:1110:21449:4011/51‑1 (MQ=0)
CGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATT < M01420:84:000000000‑ABVEH:1:1101:25896:11355/51‑1 (MQ=0)
GAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTC < M01420:84:000000000‑ABVEH:1:1113:9294:17829/51‑1 (MQ=0)
GCTGGAGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCT < M01420:84:000000000‑ABVEH:1:1108:8619:4521/51‑1 (MQ=0)
GCAGGCCGACCTGATGTTCAGCTCTGGCGTCAGCCATTTCTGGCTGGACAT < M01420:84:000000000‑ABVEH:1:1108:8416:15865/51‑1 (MQ=6)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCT < M01420:84:000000000‑ABVEH:1:2105:4111:8938/51‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1112:3256:17482/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1104:10295:14000/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATC < M01420:84:000000000‑ABVEH:1:1103:23250:21333/50‑1 (MQ=60)
GATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAT < M01420:84:000000000‑ABVEH:1:1110:21011:7564/49‑1 (MQ=60)
TCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCAT < M01420:84:000000000‑ABVEH:1:1112:13425:7505/50‑1 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1108:26857:7418/1‑51 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1101:19767:26232/1‑51 (MQ=12)
ACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCG > M01420:84:000000000‑ABVEH:1:1114:11397:13501/1‑51 (MQ=12)
CTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAGGCGC > M01420:84:000000000‑ABVEH:1:1113:10540:10343/1‑51 (MQ=13)
|
CAGCAGAACTGGACGGAACTGCTGGAGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGGCGC > NC_017635/3127381‑3127480
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
